Project: Las Torgtugueras
2023-02-22
Load Packages and Data
Cleaning Data
#write_csv(GTBK_data, file = "/data/GTBK_data")Visualizations
GTBK_data %>%
group_by(especie_nombre_latino) %>%
count() ## # A tibble: 5 × 2
## # Groups: especie_nombre_latino [5]
## especie_nombre_latino n
## <chr> <int>
## 1 Caretta caretta 2
## 2 Chelonia mydas 848
## 3 Eretmochelys imbricata 7
## 4 Lepidochelys olivacea 15
## 5 <NA> 8Visualizations
buis_2022 %>%
mutate(species = case_when(
sp == "HB" ~ "Eretmochelys imbricata",
sp == "GR" ~ "Chelonia mydas")
) %>%
ggplot(aes(x = species, y = cclnuct, fill = species)) +
geom_violin() +
scale_fill_manual(values = c("chartreuse4", "hotpink4")) +
theme_minimal() +
coord_flip () +
labs(title = "Average Curved Carapace Length of Green and Hawksbill Sea Turtles",
subtitle = "Reproductive Females Measured During 2022 Nesting Season on Buck Island, USVI",
x = "Species",
y = "Curved Carapace Length (cm)",
fill = "Species")## Warning: Removed 10 rows containing non-finite values (`stat_ydensity()`).
buis_2022 %>%
mutate(species = case_when(
sp == "HB" ~ "Eretmochelys imbricata",
sp == "GR" ~ "Chelonia mydas")
) %>%
ggplot(aes(x = species, y = cclnuct, fill = species)) +
geom_boxplot() +
scale_fill_manual(values = c("chartreuse4", "hotpink4")) +
theme_minimal() +
coord_flip () +
labs(title = "Average Curved Carapace Length of Green and Hawksbill Sea Turtles",
subtitle = "Reproductive Females Measured During 2022 Nesting Season on Buck Island, USVI",
x = "Species",
y = "Curved Carapace Length (cm)",
fill = "Species")## Warning: Removed 10 rows containing non-finite values (`stat_boxplot()`).
GTBK_data %>%
filter(especie_nombre_latino == "Chelonia mydas" |
especie_nombre_latino == "Eretmochelys imbricata" |
especie_nombre_latino == "Lepidochelys olivacea" |
especie_nombre_latino == "Caretta caretta") %>%
ggplot(aes(x = especie_nombre_latino, y = a_c_c, fill = especie_nombre_latino)) +
geom_boxplot() +
scale_fill_manual(values = c("goldenrod1","chartreuse4", "hotpink4","cornflowerblue")) +
theme_minimal() +
coord_flip() +
facet_wrap(~ geografía) +
labs(title = "Curved Carapace Length Measurements of Four Sea Turtle Species",
subtitle = "Monitored by GTBK in Kino Bay, Mexico between 2010-2023",
x = "Species",
y = "Curved Carapace Length (cm)",
fill = "Species")## Warning: Removed 1 rows containing non-finite values (`stat_boxplot()`).
GTBK_data %>%
filter(numero_recaptura %in% c(2, 3, 4)) %>%
ggplot(aes(x = numero_recaptura)) +
geom_bar()
GTBK_data %>%
filter(numero_recaptura %in% c(2, 3, 4)) %>%
ggplot(aes(x = numero_recaptura, fill = sexo_correcto)) +
geom_bar()
GTBK_data %>%
filter(numero_recaptura %in% c(1, 2, 3, 4)) %>%
filter(especie_nombre_latino == "Chelonia mydas" |
especie_nombre_latino == "Eretmochelys imbricata" |
especie_nombre_latino == "Caretta caretta" |
especie_nombre_latino == "Lepidochelys olivacea") %>%
ggplot(aes(x = numero_recaptura, fill = especie_nombre_latino)) +
geom_bar() +
scale_fill_manual(values = c("firebrick2", "darkseagreen", "royalblue4", "yellow2")) +
theme_minimal() +
labs(title = "Number of Sea Turtle Recaptures by GTBK",
subtitle = "Of Four Sea Turtle Species in Kino Bay, Mexico",
x = "Number of Times Recaptured",
y = "Number of Turtles",
fill = "Species")
# recapture_tibble <- GTBK_data %>%
# group_by(marca_nombre) %>%
# select(nombre_tortuga, fecha, especie, area_de_monitoreo, marca_nombre)
#
#
# recapture_tibble %>%
# group_by(marca_nombre) %>%
# summarize(marca_nombre)GTBK_data %>%
group_by(especie_nombre_latino) %>%
count (sexo_correcto)## # A tibble: 9 × 3
## # Groups: especie_nombre_latino [5]
## especie_nombre_latino sexo_correcto n
## <chr> <chr> <int>
## 1 Caretta caretta Indefinido 2
## 2 Chelonia mydas Hembra 339
## 3 Chelonia mydas Indefinido 483
## 4 Chelonia mydas Macho 26
## 5 Eretmochelys imbricata Indefinido 7
## 6 Lepidochelys olivacea Hembra 10
## 7 Lepidochelys olivacea Indefinido 1
## 8 Lepidochelys olivacea Macho 4
## 9 <NA> <NA> 8# GTBK_2018_2023 %>%
# group_by(especie_nombre_latino) %>%
# count(Sexo)
# GTBK_2010_2018 %>%
# group_by(Especie) %>%
# count(Sexo)
buis_2022 %>%
group_by(sp) %>%
count(sex)## # A tibble: 2 × 3
## # Groups: sp [2]
## sp sex n
## <chr> <chr> <int>
## 1 GR female 27
## 2 HB female 29GTBK_data %>%
filter(numero_recaptura == 1) %>%
group_by(especie_nombre_latino) %>%
count (sexo_correcto)## # A tibble: 9 × 3
## # Groups: especie_nombre_latino [5]
## especie_nombre_latino sexo_correcto n
## <chr> <chr> <int>
## 1 Caretta caretta Indefinido 2
## 2 Chelonia mydas Hembra 248
## 3 Chelonia mydas Indefinido 380
## 4 Chelonia mydas Macho 23
## 5 Eretmochelys imbricata Indefinido 7
## 6 Lepidochelys olivacea Hembra 10
## 7 Lepidochelys olivacea Indefinido 1
## 8 Lepidochelys olivacea Macho 4
## 9 <NA> <NA> 1GTBK_data %>%
filter(especie_nombre_latino != "NA") %>%
filter(numero_recaptura == 1) %>%
ggplot(aes(x = sexo_correcto,
fill = sexo_correcto)) +
geom_bar() +
facet_wrap( ~ especie_nombre_latino,
# <- fct_relevel(especie_nombre_latino,
# "Caretta caretta",
# "Eretmochelys imbricata",
# "Lepidochelys olivacea",
# "Chelonia mydas"),
scales = "free_y") +
labs(title = "Species and Sex Distribution",
subtitle = "of turtles captured in Kino Bay",
x = "sex",
y = "number of individuals",
fill = "sex") +
scale_fill_manual(values = c("#cd4071","#feca8d", "#721f81", "#000004"))
naniar::gg_miss_var(GTBK_data)
visdat::vis_miss(GTBK_data)## Warning: Raster pixels are placed at uneven horizontal intervals and will be shifted
## ℹ Consider using `geom_tile()` instead.
visdat::vis_miss(GTBK_2018_2023)
GTBK Recapture Visualizations
# they went out 880 times total.
# There are 188 instances of recaptures
GTBK_data <- GTBK_data %>%
mutate(mes = month(fecha)) %>%
mutate(año = year(fecha))
GTBK_outings <- GTBK_data %>%
group_by(mes) %>%
count(mes)
GTBK_recapturas <- GTBK_data %>%
filter(numero_recaptura %in% c(2, 3, 4)) %>%
group_by(mes) %>%
count(mes)
full_join(GTBK_outings, GTBK_recapturas, by = "mes") %>%
mutate(tortugas_por_esfuerzo = n.y/n.x) %>%
select(mes, tortugas_por_esfuerzo) %>%
ggplot(aes(x = mes, y = tortugas_por_esfuerzo)) +
geom_col() ## Warning: Removed 1 rows containing missing values (`position_stack()`).
# This code chunk is not to be messed with under any circumstance!
#GTBK_data <-
GTBK_data %>%
mutate(yearmonth = ym(paste(año, mes, sep = "-")))## Warning: There were 3 warnings in `mutate()`.
## The first warning was:
## ℹ In argument: `yearmonth = ym(paste(año, mes, sep = "-"))`.
## ℹ In group 1: `marca_nombre = ""`.
## Caused by warning:
## ! 1 failed to parse.
## ℹ Run ]8;;ide:run:dplyr::last_dplyr_warnings()dplyr::last_dplyr_warnings()]8;; to see the 2 remaining warnings.## # A tibble: 880 × 39
## # Groups: marca_nombre [767]
## nombre_to…¹ estac…² fecha area_…³ posic…⁴ hora_…⁵ especie peso
## <chr> <chr> <dttm> <chr> <chr> <chr> <chr> <dbl>
## 1 Lencho <NA> 2010-10-11 00:00:00 ISPM N28º37… 0.1458… Chelon… 15
## 2 Lili <NA> 2010-10-12 00:00:00 ISPM N28º37… <NA> Chelon… 18
## 3 Alejandra … <NA> 2010-10-12 00:00:00 ISPM <NA> <NA> Chelon… 17.5
## 4 Ana Luisa <NA> 2010-10-12 00:00:00 ISPM N28º22… <NA> Chelon… 27
## 5 Naomi Primav… 2011-03-15 00:00:00 ISPM N28371… <NA> Chelon… 19
## 6 Romelia Primav… 2011-03-16 00:00:00 ISPM N28371… <NA> Chelon… 17.6
## 7 LORAYNE Primav… 2011-03-16 00:00:00 ISPM n28221… <NA> Chelon… 21.6
## 8 profepa Verano 2012-10-08 00:00:00 choyud… <NA> <NA> Eretmo… 4
## 9 prescolina Otono 2012-05-11 00:00:00 Alcalt… N23.83… 0.5124… Chelon… 32
## 10 PAPIRINGO Invier… 2013-10-01 00:00:00 Pta. B… N28.78… 0.5277… Chelon… 42.8
## # … with 870 more rows, 31 more variables: sexo <chr>, l_r_c <dbl>,
## # l_c_c <dbl>, a_r_c <dbl>, a_c_c <dbl>, p_c <dbl>, l_p <dbl>, l_t_c <dbl>,
## # marca_nombre <chr>, marca_izquierda <chr>, fecha_inicio <dttm>,
## # hora_inicio <dbl>, hora_fin <dbl>, total_horas <dbl>, tipo_monitoreo <chr>,
## # metodologia <chr>, latitud <dbl>, longitud <dbl>,
## # unidad_utm_o_grados <chr>, hora_captura <dbl>, material_marcas <chr>,
## # marca_previa_izquierda <chr>, comentarios <chr>, …tortugas_por_tiempo <- GTBK_data %>% #counting every time they caught a turtle
filter(numero_recaptura %in% c(1, 2, 3, 4)) %>%
group_by(fecha, mes, año) %>%
drop_na(marca_nombre) %>%
summarize(turtles = n()) %>%
group_by(mes, año) %>%
summarize(total_turtles = sum(turtles, na.rm = T))## `summarise()` has grouped output by 'fecha', 'mes'. You can override using the
## `.groups` argument.
## `summarise()` has grouped output by 'mes'. You can override using the `.groups`
## argument.tiempo <- GTBK_data %>% # of times they went out
distinct(fecha, mes, año) %>%
group_by(mes, año) %>%
summarize(effort = n())## `summarise()` has grouped output by 'mes'. You can override using the `.groups`
## argument.# full_join(GTBK_outings, GTBK_recapturas, by = "mes") %>%
# mutate(tortugas_por_esfuerzo = n.y/n.x) %>%
# select(mes, tortugas_por_esfuerzo) %>%
# ggplot(aes(x = mes, y = tortugas_por_esfuerzo)) +
# geom_col() GTBK_data %>%
mutate(yearmonth = ym(paste(año, mes, sep = "-")))## Warning: There were 3 warnings in `mutate()`.
## The first warning was:
## ℹ In argument: `yearmonth = ym(paste(año, mes, sep = "-"))`.
## ℹ In group 1: `marca_nombre = ""`.
## Caused by warning:
## ! 1 failed to parse.
## ℹ Run ]8;;ide:run:dplyr::last_dplyr_warnings()dplyr::last_dplyr_warnings()]8;; to see the 2 remaining warnings.## # A tibble: 880 × 39
## # Groups: marca_nombre [767]
## nombre_to…¹ estac…² fecha area_…³ posic…⁴ hora_…⁵ especie peso
## <chr> <chr> <dttm> <chr> <chr> <chr> <chr> <dbl>
## 1 Lencho <NA> 2010-10-11 00:00:00 ISPM N28º37… 0.1458… Chelon… 15
## 2 Lili <NA> 2010-10-12 00:00:00 ISPM N28º37… <NA> Chelon… 18
## 3 Alejandra … <NA> 2010-10-12 00:00:00 ISPM <NA> <NA> Chelon… 17.5
## 4 Ana Luisa <NA> 2010-10-12 00:00:00 ISPM N28º22… <NA> Chelon… 27
## 5 Naomi Primav… 2011-03-15 00:00:00 ISPM N28371… <NA> Chelon… 19
## 6 Romelia Primav… 2011-03-16 00:00:00 ISPM N28371… <NA> Chelon… 17.6
## 7 LORAYNE Primav… 2011-03-16 00:00:00 ISPM n28221… <NA> Chelon… 21.6
## 8 profepa Verano 2012-10-08 00:00:00 choyud… <NA> <NA> Eretmo… 4
## 9 prescolina Otono 2012-05-11 00:00:00 Alcalt… N23.83… 0.5124… Chelon… 32
## 10 PAPIRINGO Invier… 2013-10-01 00:00:00 Pta. B… N28.78… 0.5277… Chelon… 42.8
## # … with 870 more rows, 31 more variables: sexo <chr>, l_r_c <dbl>,
## # l_c_c <dbl>, a_r_c <dbl>, a_c_c <dbl>, p_c <dbl>, l_p <dbl>, l_t_c <dbl>,
## # marca_nombre <chr>, marca_izquierda <chr>, fecha_inicio <dttm>,
## # hora_inicio <dbl>, hora_fin <dbl>, total_horas <dbl>, tipo_monitoreo <chr>,
## # metodologia <chr>, latitud <dbl>, longitud <dbl>,
## # unidad_utm_o_grados <chr>, hora_captura <dbl>, material_marcas <chr>,
## # marca_previa_izquierda <chr>, comentarios <chr>, …tortugas_por_tiempo <- GTBK_data %>% #counting every time they caught a turtle
filter(numero_recaptura %in% c(1, 2, 3, 4)) %>%
group_by(fecha, mes, año) %>%
drop_na(marca_nombre) %>%
summarize(turtles = n()) %>%
group_by(mes, año) %>%
summarize(total_turtles = sum(turtles, na.rm = T))## `summarise()` has grouped output by 'fecha', 'mes'. You can override using the
## `.groups` argument.
## `summarise()` has grouped output by 'mes'. You can override using the `.groups`
## argument.tiempo <- GTBK_data %>% # of times they went out
distinct(fecha, mes, año) %>%
group_by(mes, año) %>%
summarize(effort = n())## `summarise()` has grouped output by 'mes'. You can override using the `.groups`
## argument.full_join(tortugas_por_tiempo, tiempo) %>%
mutate(esfuerzo = total_turtles/effort)## Joining with `by = join_by(mes, año)`## # A tibble: 97 × 5
## # Groups: mes [13]
## mes año total_turtles effort esfuerzo
## <dbl> <dbl> <int> <int> <dbl>
## 1 1 2015 5 5 1
## 2 1 2016 3 3 1
## 3 1 2017 8 8 1
## 4 2 2015 3 3 1
## 5 2 2016 1 1 1
## 6 2 2017 4 4 1
## 7 2 2018 1 1 1
## 8 2 2020 2 2 1
## 9 2 2021 3 3 1
## 10 2 2023 1 1 1
## # … with 87 more rows # select(mes, tortugas_por_esfuerzo) %>%
# ggplot(aes(x = mes, y = tortugas_por_esfuerzo)) +
# geom_col()Turtle Photos/Memes
A Green sea turtle hatchling headed toward the sea.
A Hawksbill sea turtle laying her nest on Buck Island.